Monomeric and aggregated bacteriorhodopsin: Single-turnover proton transport stoichiometry and photochemistry

The question of the basic functional transport unit of bacteriorhodopsin (BR) has been addressed by comparing the proton pumping stoichiometry as well as the photocycle kinetics of monomeric and aggregated BR in phospholipid vesicles. When time-resolved laser spectroscopy was used in combination with the optical pH-indicator pyranine, single-turnover experiments revealed approximately 0.5-0.8 and 0.8-1.2 protons vectorially translocated per photocycling monomeric and aggregated BR molecule, respectively. Since both these values are akin and very similar to the pumping stoichiometry of crystalline BR molecules in the purple membrane, the BR monomer has been proven to be the essential transport unit. The natural arrangement of the photopigments in a crystalline array of immobilized trimers is not required for efficient vectorial proton translocation.

Nuclear magnetic resonance as a quantitative tool to study interactions in biomacromolecules

High-resolution nuclear magnetic resonance (NMR) has emerged as one of the most versatile tools for the quantitative study of structure, kinetics, and thermodynamics of biomolecules and their interactions at atomic resolution. Traditionally, nuclear Overhauser enhancements (NOEs) and chemical shift perturbation methods are used to determine molecular geometries and to identify contact surfaces, but more recently, weak anisotropic orientation, anisotropic diffusion, and scalar couplings across hydrogen bonds provide additional information.

Examples of such technologies are shown as applied to the quantitative characterization of function and thermodynamics of several biomacromolecules. In particular, (1) the structural and dynamical changes of the TipA multidrug resistance protein are followed upon antibiotic binding, (2) the trimer-monomer equilibrium and thermal unfolding of foldon, a small and very efficient trimerization domain of the T4 phagehead, is described in atomic detail, and (3) the changes of individual protein hydrogen bonds during thermal unfolding are quantitatively followed by scalar couplings across hydrogen bonds.

An easy way to include weak alignment constraints into NMR structure calculations

We have recently shown that an energy penalty for the incorporation of residual tensorial constraints into molecular structure calculations can be formulated without the explicit knowledge of the Saupe orientation tensor (Moltke and Grzesiek. J. Biomol. NMR, 1999, 15, 77-82). Here we report the implementation of such an algorithm into the program X-PLOR. The new algorithm is easy to use and has good convergence properties. The algorithm is used for the structure refinement of the HIV-1 Nef protein using 252 dipolar coupling restraints. The approach is compared to the conventional penalty function with explicit knowledge of the orientation tensor's amplitude and rhombicity. No significant differences are found with respect to speed, Ramachandran core quality or coordinate precision.

A DFT study of the interresidue dependencies of scalar J-coupling and magnetic shielding in the hydrogen-bonding regions of a DNA triplex

Scalar coupling constants and magnetic shieldings in the imino hydrogen-bonding region of Hoogsteen-Watson-Crick T.A-T and C(+).G-C triplets have been calculated as a function of the distance between proton donor and acceptor nitrogen atoms. The Fermi contact contributions to (h2)J((15)N-H...(15)N), (1)J((15)N-(1)H), and (h1)J((1)H...(15)N) were computed using density functional theory/finite perturbation theory (DFT/FPT) methods for the full base triplets at the unrestricted B3PW91/6-311G level. Chemical shifts delta((1)H) and delta((15)N) were obtained at the same level using the gauge including atomic orbital (GIAO) method for magnetic shielding. All three scalar couplings and all three chemical shifts are strongly interrelated and exhibit monotonic changes with base pair separation. These correlations are in conformity with experimental data for a 32-nucleotide DNA triplex. The results suggest that both chemical shifts and coupling constants can be used to gain information on H-bond donor-acceptor distances in nucleic acids. In addition to the DFT/FPT calculations, a simple three-orbital model of the N-H...H bond and a sum-over-states analysis is presented. This model reproduces the basic features of the H-bond coupling effect. In accordance with this model and the DFT calculations, a positive sign for the (h2)J(NN) coupling is determined from an E.COSY experiment.

Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide

Helix formation of an S-peptide analog, comprising the first 20 residues of Ribonuclease A and two additional N-terminal residues, was studied by measuring hydrogen bond (H-bond) (h3)J(NC') scalar couplings as a function of 2,2,2-trifluoroethanol (TFE) concentration. The (h3)J(NC') couplings give direct evidence for the closing of individual backbone N-H***O = C H-bonds during the TFE-induced formation of secondary structure. Whereas no (h3)J(NC') correlations could be detected without TFE, alpha-helical (i,i +4) H-bond correlations were observed for the amides of residues A5 to M15 in the presence of TFE. The analysis of individual coupling constants indicates that alpha-helix formation starts at the center of the S-peptide around residue E11 and proceeds gradually from there to both peptide ends as the TFE concentration is increased. At 60% to 90% TFE, well-formed alpha-helical H-bonds were observed for the amides hydrogens of residues K9 to Q13, whereas H-bonds of residues T5 to A8, H14, and M15 are affected by fraying. No intramolecular backbone H-bonds are present at and beyond the putative helix stop signal D16. As the (h3)J(NC') constants represent ensemble averages and the dependence of (h3)J(NC') on H-bond lengths is very steep, the size of the individual (h3)J(NC') coupling constants can be used as a measure for the population of a closed H-bond. These individual populations are in agreement with results derived from the Lifson-Roig theory for coil-to-helix transitions. The present work shows that the closing of individual H-bonds during TFE-induced helix formation can be monitored by changes in the size of H-bond scalar couplings.

Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR

Changes in the molecular conformation of proteins can result from a variety of perturbations, and can play crucial roles in the regulation of biological activity. A new solution NMR method has been applied to monitor ligand-induced changes in hydrogen bond geometry in the chicken c-Src SH3 domain. The structural response of this domain to ligand binding has been investigated by measuring trans-hydrogen bond (15)N-(13)C' scalar couplings in the free state and when bound to the high affinity class I ligand RLP2, containing residues RALPPLPRY. A comparison between hydrogen bonds in high resolution X-ray structures of this domain and those observed via (h3)J(NC') couplings in solution shows remarkable agreement. Two backbone-to-side-chain hydrogen bonds are observed in solution, and each appears to play a role in stabilization of loop structure. Reproducible ligand-induced changes in trans-hydrogen bond scalar couplings are observed across the domain that translate into changes in hydrogen bond length ranging between 0.02 to 0.12 A. The observed changes can be rationalized by an induced fit mechanism in which hydrogen bonds across the protein participate in a compensatory response to forces imparted at the protein-ligand interface. Upon ligand binding, mutual intercalation of the two Leu-Pro segments of the ligand between three aromatic side-chains protruding from the SH3 surface wedges apart secondary structural elements within the SH3 domain. This disruption is transmitted in a domino-like effect across the domain through networks of hydrogen bonded peptide planes. The unprecedented resolution obtained demonstrates the ability to characterize subtle structural rearrangements within a protein upon perturbation, and represents a new step in the endeavor to understand how hydrogen bonds contribute to the stabilization and function of biological macromolecules.

Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes

The diffusive properties of biomacromolecules within the aqueous phase of polyacrylamide gels are described. High quality NMR spectra can be obtained under such conditions. As compared to water, a fivefold reduction in the translational diffusion constant, but only a 1.6-fold decrease (1.4-fold increase) in amide-15N T2 (T1) are observed for human ubiquitin within a 10% acrylamide gel. Weak alignment of the solute macromolecules can be achieved within such gels by vertical or radial compression or by the embedding of magnetically oriented purple membrane fragments. The methods are applied to deriveresidual dipolar couplings for human HIV-1 Nef and ubiquitin.

Characterization of the hydrogen bond network in guanosine quartets by internucleotide 3hJ(NC)' and 2hJ(NN) scalar couplings

Scalar coupling correlations across hydrogen bonds with carbonyl groups as acceptors have been observed in a variety of proteins, but not in nucleic acids. Here we present a pulse scheme that allows such an observation and quantification of trans-hydrogen bond 3hJ(NC)' correlations in nucleic acid base pairs, between the imino nitrogen 15N1 and the carbonyl 13C6 nuclei within the guanine quartets of the Oxy-1.5 DNA-quadruplex. Intra- and internucleotide N-H...O=C connectivities can be traced around each guanine quartet, allowing the hydrogen bonding partners to be unambiguously assigned. Absolute values of the 3hJ(NC)' couplings are approximately 0.2 Hz as quantified by a selective long-range H(N)CO experiment and are thus on average smaller than the analogous 3hJ(NC)' couplings observed in proteins. In addition, an improved version of the pseudo-heteronuclear H(N)N-COSY [Majumdar et al. (1999) J. Biomol. NMR, 14, 67-70] is presented which allows simultaneous detection of the 15N-donor and 15N-acceptor resonances connected by 2hJ(NN) couplings in hydrogen bonds involving amino groups. Using this experiment, values ranging between 6 and 8 Hz are determined for the 2hJNN couplings between 15N2 and 15N7 nuclei in the guanine quartet. These values are not strongly influenced by the presence of a significant amount of chemical exchange broadening due to amino group rotations.

Inhibitor binding induces active site stabilization of the HCV NS3 protein serine protease domain

Few structures of viral serine proteases, those encoded by the Sindbis and Semliki Forest viruses, hepatitis C virus (HCV) and cytomegalovirus, have been reported. In the life cycle of HCV a crucial role is played by a chymotrypsin-like serine protease encoded at the N-terminus of the viral NS3 protein, the solution structure of which we present here complexed with a covalently bound reversible inhibitor. Unexpectedly, the residue in the P2 position of the inhibitor induces an effective stabilization of the catalytic His-Asp hydrogen bond, by shielding that region of the protease from the solvent. This interaction appears crucial in the activation of the enzyme catalytic machinery and represents an unprecedented observation for this family of enzymes. Our data suggest that natural substrates of this serine protease could contribute to the enzyme activation by a similar induced-fit mechanism. The high degree of similarity at the His-Asp catalytic site region between HCV NS3 and other viral serine proteases suggests that this behaviour could be a more general feature for this category of viral enzymes.

Measurement of dipolar couplings in a transducin peptide fragment weakly bound to oriented photo-activated rhodopsin

Rhodopsin-containing disks, isolated from rod outer segments of bovine retina, align at high magnetic fields with their membrane normal parallel to the magnetic field. After light-activation of rhodopsin, transient binding of the C-terminal transducin undecapeptide, selectively labeled with 15N at Leu5 and Gly9, results in residual dipolar contributions to the 1J(NH) splittings for these two residues. Both residues show 1J(NH) splittings which are smaller than in the dark-adapted or rhodopsin-free sample, and return to their isotropic values at a rate determined by the decay of the meta II state of rhodopsin. The dipolar couplings indicate that in the bound state, N-H vectors of Leu5 and Gly9 make angles of 48+/-4 degrees and 40+/-8 degrees, respectively, with the disk normal. These 'transferred' dipolar couplings potentially offer a useful method for studying the conformation and orientation of flexible, low affinity ligands when bound to oriented integral membrane receptors.

Observation of through-hydrogen-bond 2hJHC' in a perdeuterated protein

It is demonstrated that J connectivity between amide protons and hydrogen-bond-accepting carbonyl carbons can be observed in perdeuterated human ubiquitin. A selective pulse scheme is used to detect these small 2hJHC' interactions in the presence of the much larger through-covalent-bond 2JHC' and 3JHC' couplings. The ratio of the observed through-H-bond correlation intensity and the 2JHC' connectivity observed in a reference spectrum indicates 2hJHC' values of ca. 0.4-0.6 Hz, which are only slightly smaller than the corresponding 3hJNC' values. However, for technical reasons, 2hJHC' couplings are more difficult to measure than 3hJNC'.

Structural constraints from residual tensorial couplings in high resolution NMR without an explicit term for the alignment tensor

Structural restraints from residual tensorial couplings in high resolution NMR are usually incorporated into molecular structure calculation programs by an energy penalty function which depends on the knowledge of the alignment tensor. Here, we show that the alignment tensor enters in linear form into such a function. Therefore, the explicit appearance of the alignment tensor can be eliminated from the penalty function. This avoids the necessity of a determination of magnitude and rhombicity of the alignment tensor in the absence of structural information. The price for this procedure is a slightly shallower energy landscape. Simulations in the vicinity of the energy minimum for the backbone of human ubiquitin show that the reduction in curvature is on the order of a few percent.

Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy

It is shown that the recently developed quantitative J(NN)HNN-COSY experiment can be used for the direct identification of hydrogen bonds in non-canonical base pairs in RNA. Scalar(2h)J(NN)couplings across NH.N hydrogen bonds are observed in imino hydrogen bonded GA base pairs of the hpGA RNA molecule, which contains a tandem GA mismatch, and in the reverse Hoogsteen AU base pairs of the E-loop of Escherichia coli 5S rRNA. These scalar couplings correlate the imino donor(15)N nucleus of guanine or uridine with the acceptor N1 or N7 nucleus of adenine. The values of the corresponding(2h)J(NN)coupling constants are similar in size to those observed in Watson-Crick base pairs. The reverse Hoogsteen base pairs could be directly detected for the E-loop of E.coli 5S rRNA both in the free form and in a complex with the ribosomal protein L25. This supports the notion that the E-loop is a pre-folded RNA recognition site that is not subject to significant induced conformational changes. Since Watson-Crick GC and AU base pairs are also readily detected the HNN-COSY experiment provides a useful and sensitive tool for the rapid identification of RNA secondary structure elements.

Measurement of 3hJNC' connectivities across hydrogen bonds in a 30 kDa protein

A method is described which permits detection of 3hJNC' scalar couplings across hydrogen bonds in larger, perdeuterated proteins. The experiment is demonstrated for the uniformly 2H/13C/15N-enriched 30 kDa ribosome inactivating protein MAP30. The 3hJNC' interactions are smaller than 1 Hz, but their detection in an HNCO experiment is made possible through the use of constructive interference between the 15N chemical shift anisotropy and 1H-15N dipole-dipole relaxation mechanisms in a manner similar to that of recently proposed TROSY schemes. Sensitivity of the HNCO experiment depends strongly on the 15N transverse relaxation rate of the downfield 15N multiplet component and on the amide proton T1. In perdeuterated MAP30 at 40 degrees C, the average TROSY T2 was 169 ms at 750 MHz 1H frequency, and a wide range of longitudinal relaxation rates was observed for the amide protons.

NMR investigation and secondary structure of domains I and II of rat brain calbindin D28k (1-93)

Calbindin D28k, a member of the troponin C superfamily of calcium-binding proteins, contains six putative EF hand domains but binds only four calcium-atoms: one at a binding site of very high affinity and three calcium-atoms at binding sites of lower affinity. The high-affinity site could be located within domain I while domains III, IV, and V bind calcium less tightly. The recombinant protein construct calb I-II (residues 1-93) comprising the first two EF hands affords a unique opportunity to study a pair of EF hands with one site binding calcium tightly and the second site empty. A series of heteronuclear 2D, 3D and 4D high-resolution NMR experiments were applied to calb I-II, and led to the complete assignment of the 1H, 13C and 15N resonances. The secondary structure of the protein was deduced from the size of the 3JHN-Halpha coupling constants, the chemical shift indices of 1Etaalpha, 13Calpha, 13C' and 13Cbeta nuclei and from an analysis of backbone NOEs observed in 3D and 4D NOESY spectra. Four major alpha-helices are identified: Ala13-Phe23, Gly33-Ala50, Leu54-Asp63, Val76-Leu90, while residues Ala2-Leu6 form a fifth, flexible helical segment. Two short beta-strands (Tyr30-Glu32, Lys72-Gly74) are found preceding helices B and D and are arranged in an anti-parallel interaction. Based on these data a structural model of calb I-II was constructed that shows that the construct adopts a tertiary structure related to other well-described calcium-binding proteins of the EF-hand family. Surprisingly, the protein forms a homodimer in solution, as was shown by its NMR characterization, size-exclusion chromatography and analytical ultra-centrifugation studies.

A doublet-separated sensitivity-enhanced HSQC for the determination of scalar and dipolar one-bond J-couplings

A simple, sensitivity-enhanced HSQC experiment is described which separates the upfield and downfield components in the indirect dimension into different subspectra. The sequence is similar to the generalized TROSY scheme; however, decoupling of the X-nucleus is used during detection. A detailed analysis of relaxation effects, precision and sensitivity of the method is presented. The approach is demonstrated in a two-dimensional water flip-back 1H-15N HSQC which measures 1JHN splittings in isotropic and oriented samples of ubiquitin and the hepatitis C protease. The results are in excellent agreement with splittings obtained from a conventional 1H-coupled HSQC.

The signal transducer gp130: solution structure of the carboxy-terminal domain of the cytokine receptor homology region

The transmembrane glycoprotein gp130 is the common signal transducing receptor subunit of the interleukin-6-type cytokines. It is a member of the cytokine-receptor superfamily predicted to consist of six domains in its extracellular part. The second and third domain constitute the cytokine-binding module defined by a set of four conserved cysteines and a WSXWS motif, respectively. The three-dimensional structure of the carboxy-terminal domain of this region was determined by multidimensional NMR. The domain consists of seven beta-strands constituting a fibronectin type III-like topology. The structure reveals that the WSDWS motif of gp130 is part of an extended tryptophan/arginine zipper which modulates the conformation of the CD loop.

Determination of backbone nitrogen-nitrogen J correlations in proteins

Recently, a quantitative J correlation technique has been presented which makes use of homonuclear Hartmann-Hahn cross-polarization (TOCSY) to measure (3)J(C)'(C)' in proteins isotopically enriched with (13)C [Grzesiek, S. and Bax, A. (1997) J. Biomol. NMR, 9, 207-211]. Since homonuclear Hartmann-Hahn is twice as fast as conventional COSY transfer, this method is much less sensitive to transverse relaxation, which is the principal limiting factor in achieving long-range J-coupling correlations in macromolecules. Here we describe a similar experiment which is used to measure(3) J(NN) coupling constants between sequential amide(15) N nuclei in the backbone of ubiquitin. As expected from the low magnetic moment of (15)N, the (3)J(NN) coupling constants are exceedingly small, with values between 0.14 and 0.36 Hz for residues in β-conformations and values below 0.15 Hz for residues in α-conformations. In contrast to what is expected from a Karplus-type dependence on the backbone angle ψ, large differences in the values of(3) J(NN) are observed for a number of residues with very similar backbone ψ angles. A quantitative description of statistical and systematic errors, in particular of relaxation effects during the TOCSY transfer, shows that these differences are highly significant.

The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA

The three-dimensional solution structure has been determined by NMR spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose secondary structure consists of three helical stems and a central junction loop. The NMR data reveal that the conserved structural core of the protein, which consists of a bundle of three alpha-helices and a two-stranded parallel beta-sheet four residues in length, is nearly the same as the solution structure determined for the non-liganded form of the protein. There are however, substantial chemical shift perturbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and the first strand of parallel beta-sheet. Substantial shift perturbations are also observed in the N-terminal end of alpha-helix 1, the intervening loop that bridges helices 2 and 3, and alpha-helix 3. The four contact regions identified by the shift perturbation data also displayed protein-RNA NOEs, as identified by isotope-filtered three-dimensional NOE spectroscopy. The shift perturbation and NOE data not only implicate helix 3 as playing an important role in RNA binding, but also indicate that regions flanking helix 3 are involved as well. Loop 1 is of particular interest as it was found to be flexible and disordered for L11-C76 free in solution, but not in the RNA-bound form of the protein, where it appears rigid and adopts a specific conformation as a result of its direct contact to RNA.

Refined solution structure and backbone dynamics of HIV-1 Nef

The tendency of HIV-1 Nef to form aggregates in solution, particularly at pH values below 8, together with its large fraction of highly mobile residues seriously complicated determination of its three-dimensional structure, both for heteronuclear solution NMR (Grzesiek et al., 1996a, Nat Struct Biol 3:340-345) and for X-ray crystallography (Lee et al., 1996, Cell 85:931-942). Methods used to determine the Nef structure by NMR at pH 8 and 0.6 mM concentration are presented, together with a detailed description of Nef's secondary and tertiary structure. The described techniques have general applicability for the NMR structure determination of proteins that are aggregating and/or have limited stability at low pH values. Extensive chemical shift assignments are reported for backbone and side chain 1H, 13C, and 15N resonances of the HIV-1 Nef deletion mutants NEF delta 2-39, NEF delta 2-39, delta 159-173, and of NEF delta 2-39, delta 159-173 in complex with the SH3 domain of the Hck tyrosine protein kinase. Besides a type II polyproline helix, Nef's structure consists of three alpha-helices, a 3(10) helix, and a five-stranded anti-parallel beta-sheet. The analysis of 15N relaxation parameters of the backbone amide sites reveals that all the secondary structure elements are non-mobile on the picosecond to nanosecond and on the millisecond time scale. A large number of slowly exchanging amide protons provides evidence for the stability of the Nef core even on the time scale of hours. Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops. The residues of the HIV-1 protease cleavage site (W57/L58) do not exhibit large amplitude motions on the sub-nanosecond time scale, and their side chains insert themselves into a hydrophobic crevice formed between the C-terminus of helix 1 and the N-terminus of helix 2. A refined structure has been determined based on additional constraints for side-chain and backbone dihedral angles derived from a large number of three-bond J-coupling and ROE data.

A three-dimensional NMR experiment with improved sensitivity for carbonyl-carbonyl J correlation in proteins

Recently, a quantitative J correlation technique has been presented that permits measurement of 3Jc'c' in proteins isotopically enriched with 13C [Hu, J.-S. and Bax, A. (1996) J. Am. Chem. Soc., 118, 8170-8171]. Here, we describe an analogous experiment that is less sensitive to transverse 13C' relaxation, which is the principal limiting factor in all 13C-13C long-range correlation experiments on macromolecules. The new scheme utilizes homonuclear Hartmann-Hahn cross polarization (TOCSY) instead of a COSY type transfer to accomplish magnetization transfer; a description of the relevant relaxation terms is presented. The experiment is demonstrated for ubiquitin and HIV-1 Nef. The results show excellent agreement between 3Jc'c' values measured for ubiquitin with the new scheme and those reported previously. The experiment is particularly useful for distinguishing backbone phi angles that are smaller than -120 degrees from those larger than -120 degrees.

Mapping hydration water molecules in the HIV-1 protease/DMP323 complex in solution by NMR spectroscopy

A tetrahedrally hydrogen-bonded structural water molecule, water 301, is seen in the crystal structure of nearly every HIV-1 protease/inhibitor complex. Although the urea oxygen of the designed inhibitor, DMP323, mimics and replaces water 301, other water molecules are seen in the protease/DMP323 crystal structure. As a first step toward understanding how water molecules may contribute to inhibitor potency and specificity, we have recorded water-NOESY and water-ROESY spectra of the protease/ DMP323 complex. Cross relaxation rates derived from these spectra, together with interproton distances calculated from the crystal structure of the complex, were used to classify the exchange cross peaks as follows: (A) a direct NOE with a water proton, (B) an indirect NOE with water through a labile protein proton, and (C) direct exchange of an amide proton with water. Type A and B cross peaks were analyzed using three models of water dynamics: (1) two-site exchange, with water molecules randomly hopping between bound and free states, (2) bound water with internal motion, and (3) free diffusion. Using the two-site exchange model to analyze the relaxation data of the type A cross peaks, it was found that the water molecules had short residence times, ca. 500 ps. in contrast with the > 9 ns residence time estimated for water 301 in the protease/P9941 complex [Grzesiek et al. (1994) J. Am. Chem. Soc. 116, 1581-1582]. The NMR data are consistent with the X-ray observation that two symmetry-related water molecules, waters 422 and 456, are bound at the DMP323 binding site. Hence, these water molecules may help to stabilize the structure of the complex. Finally, it was found that three buried and hydrogen-bonded Thr hydroxyl protons were in slow exchange with solvent. In contrast, it was found that the DMP323 H4/H5 hydroxyl protons and the Asp25/125 carboxyl protons, which form a buried hydrogen-bonded network at the catalytic site of the protease, are in rapid exchange with solvent, suggesting that solvent can penetrate into the buried protein/inhibitor interface on the millisecond to microsecond time scale.

The CD4 determinant for downregulation by HIV-1 Nef directly binds to Nef. Mapping of the Nef binding surface by NMR

Using heteronuclear NMR spectroscopy, we demonstrate that a 13-residue peptide (MS-QIKRLLSEKKT) from the cytoplasmic tail of CD4 binds to Nef protein. This part of CD4 is critical for downregulation of CD4 by HIV-1 Nef [Aiken et al. (1994) Cell 76, 853-864]. We show that a control peptide without the central dileucine does not bind to Nef. The dependence of Nef 1H and 15N amide chemical shifts on peptide concentration indicates that the binding is in the fast chemical exchange limit, with a dissociation constant Kd of approximately 1 mM. The peptide binding site has been mapped onto the previously determined solution structure of HIV-1 Nef [Grzesiek et al. (1996) Nat. Struct. Biol. 3, 340-345] on the basis of peptide-induced chemical shift changes. It comprises amino acids W57, L58, E59, G95, G96, L97, R106, and L110. When Nef is complexed to the SH3 domain of Hck tyrosine protein kinase, the peptide binds to the same site on Nef but with slightly higher affinity (Kd approximately 0.5 mM). This indicates that the binding of CD4 and Hck SH3 to Nef are two compatible and slightly cooperative events.

The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase

The solution structure of HIV-1 Nef has been solved by multidimensional heteronuclear NMR spectroscopy. The construct employed to circumvent problems associated with aggregation was a double-deletion mutant (delta2-39, delta159-173) in which conformationally disordered regions of the protein at the N terminus and in a long solvent-exposed flexible loop were removed, without affecting the properties or structural integrity of the remainder of the protein. Despite the absence of any sequence similarity, the overall fold of Nef is reminiscent of that of the family of winged helix-turn-helix DNA binding proteins. The binding surface of Nef for the SH3 domain of Hck tyrosine protein kinase has been mapped and reveals a non-contiguous (in terms of amino-acid sequence) interaction surface. This unique feature may suggest possible avenues for drug design aimed at inhibiting the interaction between Nef and SH3 domains.

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

Spin-locked multiple quantum coherence for signal enhancement in heteronuclear multidimensional NMR experiments

For methine sites the relaxation rate of 13C-1H two-spin coherence is generally slower than the relaxation rate of the individual 13C and 1H single spin coherences. The slower decay of two-spin coherence can be used to increase the sensitivity and resolution in heteronuclear experiments, particularly those that require correlation of H alpha and C alpha chemical shifts. To avoid dephasing of the two-spin coherence caused by 1H-1H J-couplings, the 1H spin is locked by the application of a weak rf field, resulting in a spin-locked multiple quantum coherence. For a sample of calcium-free calmodulin, use of the multiple quantum approach yields significant signal enhancement over the conventional constant-time 2D HSQC experiment. The approach is applicable to many multidimensional NMR experiments, as demonstrated for a 3D 13C-separated ROESY CT-HMQC spectrum.

Solution structure of calcium-free calmodulin

The three-dimensional structure of calmodulin in the absence of Ca2+ has been determined by three- and four-dimensional heteronuclear NMR experiments, including ROE, isotope-filtering combined with reverse labelling, and measurement of more than 700 three-bond J-couplings. In analogy with the Ca(2+)-ligated state of this protein, it consists of two small globular domains separated by a flexible linker, with no stable, direct contacts between the two domains. In the absence of Ca2+, the four helices in each of the two globular domains form a highly twisted bundle, capped by a short anti-parallel beta-sheet. This arrangement is qualitatively similar to that observed in the crystal structure of the Ca(2+)-free N-terminal domain of troponin C.

Sequential backbone assignment of isotopically enriched proteins in D2O by deuterium-decoupled HA(CA)N and HA(CACO)N

It is demonstrated that sequential resonance assignment of the backbone 1H alpha and 15N resonances of proteins can be obtained without recourse to the backbone amide protons, an approach which should be useful for assignment of regions with rapidly exchanging backbone amide protons and for proteins rich in proline residues. The method relies on the combined use of two 2D experiments, HA(CA)N and HA(CACO)N or their 3D analogs, which correlate 1H alpha with the intraresidue 15N and with the 15N resonance of the next residue. The experiments are preferably conducted in D2O, where very high resolution in the 15N dimension can be achieved by using 2H decoupling. The approach is demonstrated for a sample of human ubiquitin, uniformly enriched in 13C and 15N. Complete backbone and 13C beta/1H beta resonance assignments are presented.

Flexibility and function in HIV-1 protease

HIV protease is a homodimeric protein whose activity is essential to viral function. We have investigated the molecular dynamics of the HIV protease, thought to be important for proteinase function, bound to high affinity inhibitors using NMR techniques. Analysis of 15N spin relaxation parameters, of all but 13 backbone amide sites, reveals the presence of significant internal motions of the protein backbone. In particular, the flaps that cover the proteins active site of the protein have terminal loops that undergo large amplitude motions on the ps to ns time scale, while the tips of the flaps undergo a conformational exchange on the microsecond time scale. This enforces the idea that the flaps of the proteinase are flexible structures that facilitate function by permitting substrate access to and product release from the active site of the enzyme.

Measurement of HN-H alpha J couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods

Two new methods are described for the measurement of three-bond JHNH alpha couplings in proteins isotopically enriched with 15N. Both methods leave the water magnetization in an unsaturated state, parallel to the z-axis, and therefore offer significant enhancements in sensitivity for rapidly exchanging backbone amide protons. The J couplings can be measured either from a set of constant-time 2D 1H-15N HMQC spectra, which are modulated in intensity by JHNH alpha, or from a water-flip-back version of the 3D HNHA experiment. The method is demonstrated for a sample of calcium-free calmodulin. Residues Lys75-Asp80 have JHNH alpha values in the 6-7 Hz range, suggesting that a break in the 'central helix' occurs at the same position as previously observed in solution NMR studies of Ca(2+)-ligated calmodulin.

Resonance assignment of methionine methyl groups and chi 3 angular information from long-range proton-carbon and carbon-carbon J correlation in a calmodulin-peptide complex

Several simple 3D experiments are used to provide J correlations between methionine C epsilon methyl carbons and either the C gamma H2 protons or C beta and C gamma. The intensity of the J correlations provides information on the size of the three-bond J couplings and thereby on the chi 3 torsion angle. In addition, a simple 3D version of the HMBC experiment provides a sensitive link between the C epsilon H3 methyl protons and C gamma. The methods are demonstrated for a 20 kDa complex between calmodulin and a 26-residue peptide fragment of skeletal muscle myosin light chain kinase.

1H, 13C, 15N nuclear magnetic resonance backbone assignments and secondary structure of human calcineurin B

The calmodulin- and calcium-stimulated protein phosphatase calcineurin, PP2B, consists of two subunits: calcineurin B, which binds Ca2+, and calcineurin A, which contains the catalytic site and a calmodulin binding site. Heteronuclear 3D and 4D NMR experiments were carried out on a recombinant human calcineurin B which is a 170-residue protein of molecular mass 19.3 kDa, uniformly labeled with 15N and 13C. The nondenaturing detergent CHAPS was used to obtain a monomeric form of calcineurin B. Three-dimensional triple resonance experiments yielded complete sequential assignment of the backbone nuclei (1H, 13C, and 15N). This assignment was verified by a 4D HN(COCA)NH experiment carried out with 50% randomly deuteriated and uniformly 15N- and 13C-enriched calcineurin B. The secondary structure of calcineurin B has been determined on the basis of the 13C alpha and 13C beta secondary chemical shifts, J(HNH alpha) couplings, and NOE connectivities obtained from 3D 15N-separated and 4D 13C/15N-separated NOESY spectra. Calcineurin B has eight helices distributed in four EF-hand, helix-loop-helix [Kretsinger, R. H. (1980) CRC Crit. Rev. Biochem. 8, 119-174] calcium binding domains. The secondary structure of calcineurin B is highly homologous to that of calmodulin. In comparison to calmodulin, helices B and C are shorter while helix G is considerably longer. As was observed for calmodulin in solution, calcineurin B does not have a single long central helix; rather, helices D and E are separated by a six-residue sequence in a flexible nonhelical conformation.

Measurement of amide proton exchange rates and NOEs with water in 13C/15N-enriched calcineurin B

A rapid and sensitive 2D approach is presented for measuring amide proton exchange rates and the NOE interaction between amide protons and water. The approach is applicable to uniformly 13C/15N-enriched proteins and can measure magnetization exchange rates in the 0.02 to > 20 s-1 range. The experiments rely on selective excitation of the water resonance, coupled with purging of underlying H alpha resonances, followed by NOESY- or ROESY-type transfer to amide protons, which are dispersed by the amide 15N frequencies in an HSQC-type experiment. Two separate but interleaved experiments, with and without selective inversion of the H2O resonance, yield quantitative results. The method is demonstrated for a sample of the calcium-binding protein calcineurin B. Results indicate rapid amide exchange for the five calcineurin B residues that are analogous to the five rapidly exchanging residues in the 'central helix' of the homologous protein calmodulin.

A simple and sensitive experiment for measurement of JCC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins

A simple 2D difference experiment is described that allows quantitative measurement of 13C-13C J couplings between backbone carbonyl and side-chain carbons. Precise 3JCC values were measured from data recorded in just 2 h for a 1-mM solution of the 20-kD complex between the protein calmodulin and a 26-residue synthetic peptide. The J couplings aid in determining the chi 1 angles of valine, isoleucine and threonine residues, and in making stereospecific assignments of the Val C gamma methyl groups. Error analysis indicates that the uncertainty in the derived J couplings is generally less than ca. 0.3 Hz.

Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins

Experiments and procedures are described that greatly alleviate the sequential assignment process of uniformly 13C/15N-enriched proteins by determining the type of amino acid from experiments that correlate side chain with backbone amide resonances. A recently proposed 3D NMR experiment, CBCA(CO)NH, correlates C alpha and C beta resonances to the backbone amide 1H and 15N resonances of the next residue (Grzesiek, S. and Bax, A. (1992) J. Am. Chem. Soc., 114, 6291-6293). An extension of this experiment is described which correlates the proton H beta and H alpha resonances to the amide 1H and 15N resonances of the next amino acid, and a detailed product operator description is given. A simple 2D-edited constant-time HSQC experiment is described which rapidly identifies H beta and C beta resonances of aromatic or Asn/Asp residues. The extent to which combined knowledge of the C alpha and C beta chemical shift values determines the amino acid type is investigated, and it is demonstrated that the combined C alpha and C beta chemical shifts of three or four adjacent residues usually are sufficient for defining a unique position in the protein sequence.

Isotope-edited multidimensional NMR of calcineurin B in the presence of the non-deuterated detergent CHAPS

At the concentration needed for NMR, the calcium-saturated form of calcineurin B dissolved in water shows resonance line widths that indicate aggregation of this protein. Although the line width or aggregation state can be influenced to some degree by temperature, pH, and salt concentrations, in the absence of detergent no conditions could be found where the protein behaved as a monomeric unit. In the presence of a 10- to 20-fold molar excess of the zwitterionic detergent 3-[(3-cholamidopropyl)-dimethyl-ammonio]-1-propanesulfonate (CHAPS), resonance line widths were considerably narrower and were compatible with a protein of approximately 25 kDa. The presence of the NMR signals of the non-deuterated CHAPS does not interfere with modern isotope-directed NMR studies as the signals from protons not attached to 15N or 13C are removed by isotope filtering and purge pulses.

1H, 13C, and 15N NMR backbone assignments and secondary structure of human interferon-gamma

1H, 13C, and 15N NMR assignments of the protein backbone of human interferon-gamma, a homodimer of 31.4 kDa, have been made using the recently introduced three-dimensional (3D) triple-resonance NMR techniques. It is shown that, despite the approximately 40-50-Hz 13C alpha and 1H alpha line widths of this high molecular weight dimer and the extensive overlap in the 1H alpha and 13C alpha spectral regions, unique sequential assignments can be made on the basis of combined use of the 3D HNCO, HNCA, HN(CO)CA, and HCACO constant-time experiments, the 15N-separated 3D NOESY-HMQC, and the 3D HOHAHA-HMQC experiments. Analysis of the 15N-separated 3D NOESY-HMQC and 13C/15N-separated four-dimensional (4D) NOESY-HMQC spectra together with the secondary C alpha and C beta chemical shifts yielded extensive secondary structure information. The NMR-derived secondary structure essentially confirms results of a recently published low-resolution crystal structure [Ealick et al. (1991) Science 252, 698-702], i.e., six helices in the monomer which are mostly alpha-helical in nature, no beta-sheets, a long flexible loop between helices A and B, and a very hydrophobic helix C. The functionally important carboxy terminus, which was not observed in the X-ray study, does not adopt a rigid conformation in solution. A high degree of internal mobility, starting at Pro-123, gives rise to significantly narrower resonance line widths for these carboxy-terminal residues compared to the rest of the protein.

Transmembrane location of retinal in bacteriorhodopsin by neutron diffraction

The transmembrane location of the chromophore of bacteriorhodopsin was obtained by neutron diffraction on oriented stacks of purple membranes. Two selectively deuterated retinals were synthesized and incorporated in bacteriorhodopsin by using the retinal- mutant JW5: retinal-d11 (D11) contained 11 deuterons in the cyclohexene ring, and retinal-d5 (D5) had 5 deuterons as close as possible to the Schiff base end of the chromophore. The membrane stacks had a lamellar spacing of 53.1 A at 86% relative humidity. Five orders were observed in the lamellar diffraction pattern of the D11, D5, and nondeuterated reference samples. The reflections were phased by D2O-H2O exchange. The absolute values of the structure factors were nonlinear functions of the D2O content, suggesting that the coherently scattering domains consisted of asymmetric membrane stacks. The centers of deuteration were determined from the observed intensity differences between labeled and unlabeled samples by using model calculations and Fourier difference methods. With the origin of the coordinate system defined midway between consecutive intermembrane water layers, the coordinates of the center of deuteration of the D11 and D5 label are 10.5 +/- 1.2 and 3.8 +/- 1.5 A, respectively. Alternatively, the label distance may be measured from the nearest membrane surface as defined by the maximum in the neutron scattering length density at the water/membrane interface. With respect to this point, the D11 and D5 labels are located at a depth of 9.9 +/- 1.2 and 16.6 +/- 1.5 A, respectively. The chromophore is tilted with the Schiff base near the middle of the membrane and the ring closer to the membrane surface. The vector connecting the two label positions in the chromophore makes an angle of 40 +/- 12 degrees with the plane of the membrane. Of the two possible orientations of the plane of the chromophore, which is perpendicular to the membrane plane, only the one in which the N----H bond of the Schiff base points toward the same membrane surface as the vector from the Schiff base to the cyclohexene ring is compatible with the known tilt angle of the polyene chain.

delta pH-induced fluorescence quenching of 9-aminoacridine in lipid vesicles is due to excimer formation at the membrane

The fluorescence of 9-aminoacridine (9-AA) is quenched in vesicular suspensions containing negatively charged lipid headgroups (e.g., phosphatidylserine) upon imposition of a transmembrane (inside acidic) pH-gradient. It is shown that this fluorescence loss is accompanied by the formation of 9-AA dimers that undergo a transition in the dimer excited state to a dimer-excimer state. This result has been obtained on the basis of the specific dimer fluorescence excitation and hypochromic absorbance spectra that are redshifted by maximally 275 cm-1 (4.4 nm) with respect to the corresponding monomer spectra, as well as by the detection of the characteristic broad excimer emission band, centered at 560 nm. The existence of the spectrally distinct dimer-excimer is further corroborated by fluorescence life-time measurements that indicate an increased lifetime of up to 24 ns for this complex as compared with the normal monomer fluorescence lifetime of 16 ns. The formation of this dimer-excimer complex from the monomers can be reversed completely and the original monomeric spectral properties restored after the abolishment of the electrochemical proton gradient. In addition to the delta pH-induced dimer redshift in absorbance and fluorescence excitation, a further small redshift in monomer absorbance, fluorescence excitation, and emission spectra is observed due solely to the presence of the negatively charged phospholipid headgroups.

Genetic transfer of the pigment bacteriorhodopsin into the eukaryote Schizosaccharomyces pombe

The gene encoding for bacterio-opsin (bop gene) from Halobacterium halobium has been introduced in a yeast expression vector. After transformation in Schizosaccharomyces pombe, bacterio-opsin (BO) is expressed and was detected by antisera. The precursor protein of BO (pre-BO) is processed by cleavage of amino acids at the N-terminal end as in H. halobium. Addition of the chromophore, retinal, to the culture medium results in a slight purple colour of the yeast cells indicating the in vivo regeneration of BO to bacteriorhodopsin (BR) and its incorporation into membranes. Therefore, in contrast to the expression in E. coli, isolation of the membrane protein and reconstitution in lipid vesicles is not necessary for functional analysis. The kinetics of the ground state signal of the photocycle BR in protoplasts is demonstrated by flash spectroscopy and is comparable to that of the natural system. The present investigation shows for the first time the transfer of an energy converting protein from archaebacteria to eukaryotes by genetic techniques. This is a basis for further studies on membrane biogenesis, genetics, and bioenergetics by analysis of in vivo active mutants.

The 'delta pH'-probe 9-aminoacridine: response time, binding behaviour and dimerization at the membrane

The fluorescence quenching of 9-aminoacridine (9-AA) after imposition of a transmembrane pH gradient (inside acidic) in liposomes has been investigated for a number of different lipid systems. The initial fluorescence decrease after a rapid pH jump, induced in the extravesicular medium by a stopped-flow mixing technique, was ascribed to a response of 9-AA to the imposed pH gradient and not to changes in the vesicular system itself. Time constants for this fluorescence quenching are in the range of several hundred milliseconds at 25 degrees C. Fluorescence recovery which should be correlated to the dissipation of the pH gradient occurs in the 100 s time range and is 10-30-times faster than the delta pH decay monitored with the entrapped hydrophilic pH-indicator dye pyranine. The quenching was severely hindered below the lipid phase transition of dipalmitoylphosphatidylglycerol. No delta pH-induced quenching was obtained in lipid vesicles containing only zwitterionic, net uncharged phosphatidylcholine headgroups. For the occurrence of quenching, the presence of negatively charged headgroups, i.e. phosphatidylglycerol or phosphatidylserine, was necessary. The extent of quenching, at a specific pH difference applied, had a cooperative dependency (Hill coefficient approximately 2) on the number of negative headgroups in the membrane and on the concentration of unquenched (unbound) 9-AA molecules. The concentration of quenched 9-AA molecules was furthermore proportional to the number of dimer-excimer complexes of 9-AA which are formed during the quenching process.

Dependency of delta pH-relaxation across vesicular membranes on the buffering power of bulk solutions and lipids

The dependency of delta pH-relaxation kinetics across the membrane of sonicated small phospholipid vesicles on the concentration of internally entrapped buffer has been investigated by means of the pH-indicator dye pyranine. A very high contribution of lipid headgroups to the internal buffering power of the liposomes is observed, amounting to an equivalent phosphate buffer concentration of 110 mM. This localized two-dimensional proton/hydroxide ion reservoir must be considered in any determination of the H+/OH- permeability coefficient. Furthermore, it could have significance for energy-transduction across biological membranes. From the established linear relation between delta pH-relaxation rates and buffering power, net H+/OH- permeabilities of 3 X 10(-3) cm/s for soybean phospholipid (SBPL) and 1 X 10(-4) cm/s for diphytanoyl phosphatidylcholine (diphytanoyl PC) vesicles at pH 7.2 as well as buffering powers per lipid molecule of 6 X 10(-2) (pH-unit)-1 (SBPL) and 4 X 10(-2) (pH-unit)-1 (diphytanoyl PC) are calculated. In the case of diphytanoyl PC vesicles, delta pH-decay is accelerated by the presence of chloride ions.